I think in the emulator menu there is an option to save the controller config. I haven’t actually tested if it’s working in 3.3, but I assume it is.
for the issue you were having logging in as root, I just read in another thread that there may be an SSH_enable setting or something like that in config.txt. Maybe try enabling that then try connecting again with filezilla. For me it makes the whole process much smoother.
^^ my other hobby